I just want to make sure that I got this right and have it in the same format that you have suggested.
This is what I came up with though I think it might not pick up on the midnight values but I'm hoping that it does.
The data looks good I checked a few outputs based on the employee info but I just wanted to get the formatting correct.
SELECT DISTINCT (ttl.employee_id),COUNT(distinct ttl.hu_id) [Cartons Loaded]
FROM t_tran_log ttl with(nolock)
LEFT OUTER JOIN t_employee emp with(nolock) ON ttl.employee_id = emp.id
WHERE ttl.tran_type IN ('343','372')
AND emp.dept = '2nd'
AND ttl.end_tran_date = DATEADD(d,DATEDIFF(d,0, GETDATE()),-1)
AND ttl.end_tran_date < DATEADD(d,DATEDIFF(d,0, GETDATE()),+1)
AND ttl.end_tran_time > '1900-01-01 15:30:00.000'
AND ttl.location_id_2 LIKE 'D%'
OR ttl.tran_type IN ('343','372')
AND ttl.employee_id = 'WCS'
AND ttl.end_tran_date = DATEADD(d,DATEDIFF(d,0, GETDATE()),-1)
AND ttl.end_tran_date < DATEADD(d,DATEDIFF(d,0, GETDATE()),+1)
AND ttl.end_tran_time < '1900-01-01 15:30:00.000'
AND ttl.location_id_2 LIKE 'D%'
OR ttl.tran_type IN ('343','372')
AND emp.dept = '2nd'
AND ttl.end_tran_date = CAST(GETDATE() AS DATE)
AND ttl.end_tran_date < DATEADD(d,DATEDIFF(d,0, GETDATE()),+1)
AND ttl.end_tran_time < '1900-01-01 02:30:00.000'
AND ttl.location_id_2 LIKE 'D%'
OR ttl.tran_type IN ('343','372')
AND ttl.employee_id = 'WCS'
AND ttl.end_tran_date = CAST(GETDATE() AS DATE)
AND ttl.end_tran_date < DATEADD(d,DATEDIFF(d,0, GETDATE()),+1)
AND ttl.end_tran_time < '1900-01-01 02:30:00.000'
AND ttl.location_id_2 LIKE 'D%'
GROUP BY ttl.employee_id ORDER BY ttl.employee_id